rs11568828

Positions:

• chr17-63918913-T-C
• chr17-63918913-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000647774.1(ENSG00000285947):​c.287-407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,529,780 control chromosomes in the GnomAD database, including 9,160 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.090 (732 hom., cov: 33)
  • Exomes 𝑓: 0.11 (8428 hom.)
• Consequence: ENSG00000285947 ENST00000647774.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 3.25

Genes affected

ENSG00000285947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 17-63918913-T-C is Benign according to our data. Variant chr17-63918913-T-C is described in ClinVar as [Benign]. Clinvar id is 1239137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63918913T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285947	ENST00000647774.1	c.287-407A>G		intron_variant				ENSP00000497443.1

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13759 AN: 152034 Hom.: 733 Cov.: 33

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0489

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.106 AC: 146018 AN: 1377628 Hom.: 8428 AF XY: 0.105 AC XY: 71819 AN XY: 685586

Gnomad4 AFR exome AF: 0.0470

Gnomad4 AMR exome AF: 0.0733

Gnomad4 ASJ exome AF: 0.145

Gnomad4 EAS exome AF: 0.0366

Gnomad4 SAS exome AF: 0.0523

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.0904 AC: 13762 AN: 152152 Hom.: 732 Cov.: 33 AF XY: 0.0886 AC XY: 6588 AN XY: 74394

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.0499

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0938 Hom.: 84

Bravo AF: 0.0887

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	This variant is associated with the following publications: (PMID: 28910730, 16517055) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11568828; hg19: chr17-61996273;